Input and runtime details for job 8257533 (precomputed example)

Sequence input

	sRNA sequences		[.fa]
	Putative target sequences (organism of interest)		[.fa]
	Extract sequences around		start codon
	nt up (1-300)		200
	nt down (1-300)		100

CopraRNA parameters

	Consensus prediction		off
	p-value combination		no
	p-value filtering (0=off)		0

IntaRNA parameters

	Target folding window size		150
	Target max. basepair distance		100

Job ID 8257533 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:34:31 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:34:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:30:38 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:30:45 CET 2018
	Job Completed		@ Fri Feb 16 22:31:01 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=8257533&toolName=CopraRNA ( 30 days expiry )

Description of the job

LhrA2

Output download complete results [zip]

Downloadable files

	CopraRNA result table:		[csv]
	Functional enrichment file		[txt]
	Auxiliary enrichment file		[csv]
	mRNA regions plot		[png] [pdf] [ps]
	sRNA regions plot		[png] [pdf] [ps]
	Functional annotation chart		[html] [pdf]
	Phylogenetic conservation		[png] [pdf]
	16S rDNA tree		[txt] [svg]

mRNA region plot

sRNA region plot

Annot. chart

Conserved, identified interactions for NC_003210 Listeria monocytogenes EGD-e

Select: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 101-110 111-120 121-130 131-140 141-150 151-160 161-170 171-180 181-190 191-200 all

Sort by selecting a column name:

Rank	CopraRNA p-value	CopraRNA fdr value	Locus Tag	Gene Name	Energy [kcal/mol]	IntaRNA p-value	Position mRNA	Position sRNA	Annotation
184	0.05355	0.7607	lmo2119	N/A	-15.99	0.064071	3 -- 81	95 -- 171		_____________2_________________________82\n_____________\|_________________________\|\n_________5'-CU______U______GU__________AUUAC...CCA-3'\n______________UGGGAU_AGUGAA__GACAGAUAGU\n______________\|\|:\|\|\|_\|:\|\|\|\|__:\|\|\|:\|\|\|:\|\n______________ACUCUA_UUACUU__UUGUUUAUUA\n3'-GUU...CGGUU______C__________________CUAAA...GGA-5'\n_____________\|_________________________\|\n_____________172_______________________94\n	18 -- 24	152 -- 158	-18.6088 kcal/mol	3.83703 kcal/mol	5.55637 kcal/mol	2 82@LB@ \| \|@LB@ 5'-CU U GU AUUAC...CCA-3'@LB@ UGGGAU AGUGAA GACAGAUAGU@LB@ \|\|:\|\|\| \|:\|\|\|\| :\|\|\|:\|\|\|:\|@LB@ ACUCUA UUACUU UUGUUUAUUA@LB@3'-GUU...CGGUU C CUAAA...GGA-5'@LB@ \| \|@LB@ 172 94@LB@@LB@@LB@Energy -15.99 kcal/mol@LB@Hybridization Energy -18.6088 kcal/mol@LB@Unfolding Energy - mRNA 3.83703 kcal/mol@LB@Unfolding Energy - sRNA 5.55637 kcal/mol@LB@@LB@Position - mRNA 3 -- 81@LB@Position - sRNA 95 -- 171@LB@Position Seed - mRNA 18 -- 24@LB@Position Seed - sRNA 152 -- 158@LB@
186	0.05422	0.7607	lmo2356	N/A	-15.92	0.066009	162 -- 205	129 -- 170	lmo2356	_____________161___________________206\n_____________\|_____________________\|\n5'-CUC...AAAGA_______AUUGAU________UUUGA...UUG-3'\n______________GAGAUGA______GUGAGGAU\n______________\|\|\|\|\|\|\|______:\|\|\|::\|:\n______________CUCUACU______UACUUUUG\n3'-GUU...GGUUA_____________________UUUAU...GGA-5'\n_____________\|_____________________\|\n_____________171___________________128\n	176 -- 182	156 -- 162	-14.0636 kcal/mol	2.1522 kcal/mol	0.916023 kcal/mol	161 206@LB@ \| \|@LB@5'-CUC...AAAGA AUUGAU UUUGA...UUG-3'@LB@ GAGAUGA GUGAGGAU@LB@ \|\|\|\|\|\|\| :\|\|\|::\|:@LB@ CUCUACU UACUUUUG@LB@3'-GUU...GGUUA UUUAU...GGA-5'@LB@ \| \|@LB@ 171 128@LB@@LB@@LB@Energy -15.92 kcal/mol@LB@Hybridization Energy -14.0636 kcal/mol@LB@Unfolding Energy - mRNA 2.1522 kcal/mol@LB@Unfolding Energy - sRNA 0.916023 kcal/mol@LB@@LB@Position - mRNA 162 -- 205@LB@Position - sRNA 129 -- 170@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 156 -- 162@LB@
188	0.05492	0.7607	lmo1246	N/A	-15.64	0.074442	171 -- 206	183 -- 211	ATP-dependent RNA helicase	_____________170_______________207\n_____________\|_________________\|\n5'-GCC...AUGAU______A__________UGACA...CCU-3'\n______________AUGAGG__AAUGAGGAC\n______________\|\|\|\|\|:__\|\|\|\|\|::\|\|\n______________UACUCU__UUACUUUUG\n3'-GUU...CCGGU______AC_________UUUAU...GGA-5'\n_____________\|_________________\|\n_____________212_______________182\n	190 -- 196	156 -- 162	-13.5081 kcal/mol	2.39769 kcal/mol	0.922045 kcal/mol	170 207@LB@ \| \|@LB@5'-GCC...AUGAU A UGACA...CCU-3'@LB@ AUGAGG AAUGAGGAC@LB@ \|\|\|\|\|: \|\|\|\|\|::\|\|@LB@ UACUCU UUACUUUUG@LB@3'-GUU...CCGGU AC UUUAU...GGA-5'@LB@ \| \|@LB@ 212 182@LB@@LB@@LB@Energy -15.64 kcal/mol@LB@Hybridization Energy -13.5081 kcal/mol@LB@Unfolding Energy - mRNA 2.39769 kcal/mol@LB@Unfolding Energy - sRNA 0.922045 kcal/mol@LB@@LB@Position - mRNA 171 -- 206@LB@Position - sRNA 183 -- 211@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 156 -- 162@LB@
189	0.05497	0.7607	lmo1156	N/A	-15.46	0.080118	37 -- 70	155 -- 186	diol dehydratase-reactivating factor large subunit	_____________36________________71\n_____________\|_________________\|\n5'-UAU...AAAUG______A__________UAUAU...CUA-3'\n______________CGGUGA_AUGAAUGAAG\n______________\|::\|\|\|_\|\|\|\|\|\|\|\|\|:\n______________GUUACU_UACUUACUUU\n3'-GUU...UGCCG______C__________UGUUU...GGA-5'\n_____________\|_________________\|\n_____________187_______________154\n	200 -- 206	158 -- 164	-15.35 kcal/mol	3.5534 kcal/mol	0.871719 kcal/mol	36 71@LB@ \| \|@LB@5'-UAU...AAAUG A UAUAU...CUA-3'@LB@ CGGUGA AUGAAUGAAG@LB@ \|::\|\|\| \|\|\|\|\|\|\|\|\|:@LB@ GUUACU UACUUACUUU@LB@3'-GUU...UGCCG C UGUUU...GGA-5'@LB@ \| \|@LB@ 187 154@LB@@LB@@LB@Energy -15.46 kcal/mol@LB@Hybridization Energy -15.35 kcal/mol@LB@Unfolding Energy - mRNA 3.5534 kcal/mol@LB@Unfolding Energy - sRNA 0.871719 kcal/mol@LB@@LB@Position - mRNA 37 -- 70@LB@Position - sRNA 155 -- 186@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 158 -- 164@LB@
190	0.0551	0.7607	lmo0641	N/A	-14.65	0.112053	196 -- 245	175 -- 211	heavy metal-transporting ATPase	_____________195_____________________246\n_____________\|_______________________\|\n5'-AUU...GAGCA______AA__U____________GAAUU...ACU-3'\n______________UAAUGA__GA_UGGAUGAAG_CA\n______________:\|\|\|\|\|__\|\|_\|\|:\|\|\|\|\|:_\|\|\n______________GUUACU__CU_ACUUACUUU_GU\n3'-GUU...UGCCG____________________U__UUAUU...GGA-5'\n_____________\|_______________________\|\n_____________212_____________________174\n	212 -- 218	158 -- 164	-12.4633 kcal/mol	2.08827 kcal/mol	0.95817 kcal/mol	195 246@LB@ \| \|@LB@5'-AUU...GAGCA AA U GAAUU...ACU-3'@LB@ UAAUGA GA UGGAUGAAG CA@LB@ :\|\|\|\|\| \|\| \|\|:\|\|\|\|\|: \|\|@LB@ GUUACU CU ACUUACUUU GU@LB@3'-GUU...UGCCG U UUAUU...GGA-5'@LB@ \| \|@LB@ 212 174@LB@@LB@@LB@Energy -14.65 kcal/mol@LB@Hybridization Energy -12.4633 kcal/mol@LB@Unfolding Energy - mRNA 2.08827 kcal/mol@LB@Unfolding Energy - sRNA 0.95817 kcal/mol@LB@@LB@Position - mRNA 196 -- 245@LB@Position - sRNA 175 -- 211@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 158 -- 164@LB@
191	0.0551	0.7607	lmo2853	N/A	-14.70	0.110014	201 -- 241	156 -- 201		_____________200_______________________________________________242\n_____________\|_________________________________________________\|\n5'-GGU...AGAAA________________________AA___U___ACGU____________UAUCC...UUC-3'\n______________GUGAG____AGAUAU_AACUGCGC__GGC_CAA_____UGAA__GAAGC\n______________:\|\|\|\|____\|\|\|:\|\|_\|\|\|\|:\|:\|__\|\|\|_\|\|\|_____\|\|\|\|__:\|\|:\|\n______________UACUC____UCUGUA_UUGAUGUG__CCG_GUU_____ACUU__UUUUG\n3'-GUU...UGCCC_____CGUA______C_________________ACUCU____AC_____UUUAU...GGA-5'\n_____________\|_________________________________________________\|\n_____________202_______________________________________________155\n	213 -- 219	178 -- 184	-28.7711 kcal/mol	7.06239 kcal/mol	14.0114 kcal/mol	200 242@LB@ \| \|@LB@5'-GGU...AGAAA AA U ACGU UAUCC...UUC-3'@LB@ GUGAG AGAUAU AACUGCGC GGC CAA UGAA GAAGC@LB@ :\|\|\|\| \|\|\|:\|\| \|\|\|\|:\|:\| \|\|\| \|\|\| \|\|\|\| :\|\|:\|@LB@ UACUC UCUGUA UUGAUGUG CCG GUU ACUU UUUUG@LB@3'-GUU...UGCCC CGUA C ACUCU AC UUUAU...GGA-5'@LB@ \| \|@LB@ 202 155@LB@@LB@@LB@Energy -14.70 kcal/mol@LB@Hybridization Energy -28.7711 kcal/mol@LB@Unfolding Energy - mRNA 7.06239 kcal/mol@LB@Unfolding Energy - sRNA 14.0114 kcal/mol@LB@@LB@Position - mRNA 201 -- 241@LB@Position - sRNA 156 -- 201@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 178 -- 184@LB@
194	0.05602	0.7607	lmo1602	N/A	-15.08	0.094256	153 -- 204	160 -- 207		_____________152_______________________________________205\n_____________\|_________________________________________\|\n5'-UUU...ACUCA_________AAAA___________A_____U____A_____UAGUA...CAA-3'\n______________GGGUAUAGA____GGA__AUAUGG__GGUG_GGAU_GAUGA\n______________:\|\|:\|\|\|\|\|____\|:\|__\|:\|:\|\|__::\|\|_:\|\|\|_:\|\|\|\|\n______________UCCGUAUCU____CUU__UGUGCC__UUAC_UCUA_UUACU\n3'-GUU...CCUAC_________GUA____GA______GG_________C_____UUUGU...GGA-5'\n_____________\|_________________________________________\|\n_____________208_______________________________________159\n	168 -- 174	191 -- 197	-27.2651 kcal/mol	6.9826 kcal/mol	13.8637 kcal/mol	152 205@LB@ \| \|@LB@5'-UUU...ACUCA AAAA A U A UAGUA...CAA-3'@LB@ GGGUAUAGA GGA AUAUGG GGUG GGAU GAUGA@LB@ :\|\|:\|\|\|\|\| \|:\| \|:\|:\|\| ::\|\| :\|\|\| :\|\|\|\|@LB@ UCCGUAUCU CUU UGUGCC UUAC UCUA UUACU@LB@3'-GUU...CCUAC GUA GA GG C UUUGU...GGA-5'@LB@ \| \|@LB@ 208 159@LB@@LB@@LB@Energy -15.08 kcal/mol@LB@Hybridization Energy -27.2651 kcal/mol@LB@Unfolding Energy - mRNA 6.9826 kcal/mol@LB@Unfolding Energy - sRNA 13.8637 kcal/mol@LB@@LB@Position - mRNA 153 -- 204@LB@Position - sRNA 160 -- 207@LB@Position Seed - mRNA 168 -- 174@LB@Position Seed - sRNA 191 -- 197@LB@
195	0.0561	0.7607	lmo2779	N/A	-14.82	0.104550	1 -- 44	150 -- 181	GTP-binding protein EngD	_____________0____________45\n_____________\|____________\|\n5'-ACG...AGCUU_________U__CUAUU...CGU-3'\n______________AUGAGAUGA_UG\n______________\|\|\|\|\|\|\|\|\|_\|\|\n______________UACUCUACU_AC\n3'-GUU...CCGGU_________U__UUUUG...GGA-5'\n_____________\|____________\|\n_____________182__________149\n	17 -- 23	164 -- 170	-12.8914 kcal/mol	1.66686 kcal/mol	0.818518 kcal/mol	0 45@LB@ \| \|@LB@5'-ACG...AGCUU U CUAUU...CGU-3'@LB@ AUGAGAUGA UG@LB@ \|\|\|\|\|\|\|\|\| \|\|@LB@ UACUCUACU AC@LB@3'-GUU...CCGGU U UUUUG...GGA-5'@LB@ \| \|@LB@ 182 149@LB@@LB@@LB@Energy -14.82 kcal/mol@LB@Hybridization Energy -12.8914 kcal/mol@LB@Unfolding Energy - mRNA 1.66686 kcal/mol@LB@Unfolding Energy - sRNA 0.818518 kcal/mol@LB@@LB@Position - mRNA 1 -- 44@LB@Position - sRNA 150 -- 181@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 164 -- 170@LB@
196	0.05638	0.7607	lmo2015	N/A	-14.78	0.106466	232 -- 254	163 -- 185	alpha-mannosidase	_____________231____________________________255\n_____________\|______________________________\|\n5'-GUA...ACUAA______________A___AGGCU_______GUUGC...UCC-3'\n______________AGAUA__AACUACG_GGC_____AGAUGAA\n______________\|\|\|:\|__\|\|\|\|\|\|:_\|\|\|_____\|\|\|\|\|\|\|\n______________UCUGU__UUGAUGU_CCG_____UCUACUU\n3'-GUU...CCGUA_____AC_______G___GUUAC_______ACUUU...GGA-5'\n_____________\|______________________________\|\n_____________186____________________________162\n	248 -- 254	163 -- 169	-25.0473 kcal/mol	4.43892 kcal/mol	11.8636 kcal/mol	231 255@LB@ \| \|@LB@5'-GUA...ACUAA A AGGCU GUUGC...UCC-3'@LB@ AGAUA AACUACG GGC AGAUGAA@LB@ \|\|\|:\| \|\|\|\|\|\|: \|\|\| \|\|\|\|\|\|\|@LB@ UCUGU UUGAUGU CCG UCUACUU@LB@3'-GUU...CCGUA AC G GUUAC ACUUU...GGA-5'@LB@ \| \|@LB@ 186 162@LB@@LB@@LB@Energy -14.78 kcal/mol@LB@Hybridization Energy -25.0473 kcal/mol@LB@Unfolding Energy - mRNA 4.43892 kcal/mol@LB@Unfolding Energy - sRNA 11.8636 kcal/mol@LB@@LB@Position - mRNA 232 -- 254@LB@Position - sRNA 163 -- 185@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 163 -- 169@LB@
197	0.05638	0.7607	lmo0344	N/A	-15.66	0.073858	267 -- 298	182 -- 211	short chain dehydrogenase	_____________266______299\n_____________\|________\|\n5'-CAG...CAGCA________UGGUA...UUU-3'\n______________AGCGGGAU\n______________\|:\|\|\|\|\|\|\n______________UUGCCCUA\n3'-GUU...ACGUA________CUCCG...GGA-5'\n_____________\|________\|\n_____________212______181\n	271 -- 277	200 -- 206	-11.8444 kcal/mol	1.0403 kcal/mol	0.330969 kcal/mol	266 299@LB@ \| \|@LB@5'-CAG...CAGCA UGGUA...UUU-3'@LB@ AGCGGGAU@LB@ \|:\|\|\|\|\|\|@LB@ UUGCCCUA@LB@3'-GUU...ACGUA CUCCG...GGA-5'@LB@ \| \|@LB@ 212 181@LB@@LB@@LB@Energy -15.66 kcal/mol@LB@Hybridization Energy -11.8444 kcal/mol@LB@Unfolding Energy - mRNA 1.0403 kcal/mol@LB@Unfolding Energy - sRNA 0.330969 kcal/mol@LB@@LB@Position - mRNA 267 -- 298@LB@Position - sRNA 182 -- 211@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 200 -- 206@LB@

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

Energy

Hybridization Energy

Unfolding Energy - mRNA

Unfolding Energy - sRNA

Position - mRNA

Position - sRNA

Position Seed - mRNA

Position Seed - sRNA

Evolutionary conservation of mRNA targets (alignment generated with Jalview)

Evolutionary conservation of sRNA (alignment generated with Jalview)

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When using CopraRNA please cite :

Patrick R. Wright, Jens Georg, Martin Mann, Dragos A. Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, and Rolf Backofen
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Nucleic Acids Research, 2014, 42 (W1), W119-W123.
Patrick R. Wright, Andreas S. Richter, Kai Papenfort, Martin Mann, Joerg Vogel, Wolfgang R. Hess, Rolf Backofen and Jens Georg
Comparative genomics boosts target prediction for bacterial small RNAs
Proc Natl Acad Sci USA, 2013, 110 (37), E3487-E3496.
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with CopraRNA version 2.1.2

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